Unfortunately, that's not the end of the story as far as software patents in Europe are concerned. Despite its name, the European Patent Office is not the patent office for the European Union: it is part of the European Patent Organisation, which is independent of the EU, and is therefore not bound by the EU's policies and decisions. This has enabled it to let in software patents by the back door, using the artificial concept of a "computer-implemented invention (CII)":

A CII is usually defined as an invention that works by using a computer, a computer network or other programmable apparatus. To qualify, the invention also needs to have one or more features which are realised wholly or partly by means of a computer program.

To be patentable, CIIs must fulfil the same basic patentability requirements as inventions in all other fields. These are set out in the European Patent Convention (EPC).

Accordingly, CIIs can be patented if:

They have technical character and solve a technical problem.
They are new.
They involve an inventive technical contribution to the prior art.

Pursuant to its longstanding practice in the area of so-called software patents, the Polish Patent Office held that the invention was not of a technical character and therefore was not patentable, despite the fact that the European Patent Office had granted a European patent for the same invention. In other words, the Polish Patent Office refused to issue a patent to an applicant already approved by the EPO.

This incompatibility between the rulings of the Polish Patent Office and the EPO led a higher Polish court, the Polish Supreme Administrative Court, to intervene. It has now reviewed the case and issued a revocation of the earlier decision by the Polish Patent Office, implicitly giving precedence to the EPO on the matter.
The reasoning of the Polish Supreme Administrative Court seems to be essentially that technology has moved on, and therefore the Polish patent system should take account of that by allowing software patents now, just as the EPO does:

The [upper] court also noted that great technological advances across many industries have been made in recent years, which must have an effect on the practice of the Polish Patent Office. Thus, the Polish Patent Office, while conforming to the provisions of Polish patent law, should change its approach on the subject matter of the technology.

But that's an absurd argument. Software has been around for half a century: the basic ideas underlying it haven't changed, nor have the sound reasons for excluding it from patentability been superseded -- it's just become much more widespread. If anything, that's a further argument against allowing software patents.

To grant software patents now would be like granting patents on written phrases simply because writing has "moved on", and literacy has become more widespread. Clearly that would stifle creativity, since writers would then have to worry about "infringing" on patented elements of their craft, and lawsuits would break out between authors claiming their ideas were "stolen", when in fact they were simply part of their cultural heritage.

Similarly, in the digital world, allowing software patents would mean that programmers would run the risk of "infringing" just for using basic programming building blocks in their creations. And that, of course, is precisely what is starting to happen on a massive scale in jurisdictions that do allow software patents: litigation is making innovation increasingly hard, especially for start-ups without the resources to fight long legal battles, or patent portfolios to use for striking licensing deals.

Given Poland's glorious recent past in defending Europe from dangerous ideas like ACTA and software patents, it's sad to see the country's courts trying to make its own citizens subject to the EPO and its maximalist views that more or less anything is patentable. Perhaps it's time to take to the streets again....

Re:

when will people learn? if there is a way for something that no one wants, other than the proposer or the company/industry that wants it, a way is always found. that seems to be particularly true if the introduction of whatever that something is, is detrimental to the ordinary people and their rights.

Our anti-patent and anti-IP-maximalism NGOs are quite strong right now in Poland due to ACTA backlash. And such topics continue to appear in mainstream media. Let's hope that the media will become as interested in this as in the case of ACTA and the government will backtrack on this absurd idea.

From the US

I feel for you guys, and I wish I could have gotten someone to care about software patents in the US before they became intrenched.
Instead, all I found were denials and gold-diggers. They've changed their opinions now, but it's too late.

Just wait until someone comes up with a machine that can assemble inventions up from the molecule if need be. Copyright and patent violations downloaded all in one go! :P

I'm serious when I say that you'll eventually have shooting wars over that kind of technology and patents. When you're losing money and have the strings to pull, you can imagine it being more than a little tempting to get the military involved. Look up "banana republic" or "United fruit company" or "FDA raids" to get an idea of how this goes.